Why does parenting an element deform all of the vertices in Grease Pencil?
Can you upload a .blend file - it may help to see exactly what is happening.

I've had similar issues with GP and rigging.  From what I understand, when you create a bone, or armature, they default with their own local axis (which point in a different direction to the world axis).  When you parent the Grease Pencil object to the bone, it inherits the object's local axis and flips, turns, or moves.

Possible Fix:
You can try adding a 90 or 270 to the rotation on that object to see if it comes back.

Future prevention:
As soon as you click on parent: armature with automatic weights (or something similar), there will be a small window that appears at the bottom left corner of the screen - you can click "Keep Transform" - this my prevent your geometry from getting away from you.